[gmx-users] Abnormal popc struture after inserting protein
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 2 12:23:13 CEST 2008
minnale wrote:
>
>
>
>
> Thanks to Justin for comment about my problem
> I will tell you clearly
> 1. Initially POPC bilayer taken from Tieleman website and run the
> simulation for 5ns.
> 2. Protein also has taken and simulated for 9ns actually this contain
> 10 helices among that 10 helices two helices have taken, because i
> want only 2 and generated .top file for 2 helices by using *pdb2gmx
> command.
> 3. By using VMD orient 2 helices properly in POPC bilayer
> 4. BY using genbox command these helices embedded into POPC
> 5. Minimisation has done, it ran fine without error but it didnt reach
> FMAX<1000
> 6. Ran restarin with fc1000 showed the abnrmal POPC and water
> molecules stucture.
>
>
All of that seems reasonable enough. There are two possibilities that
come to mind for things that might be of issue:
1. Run the simulation longer (see my previous message).
2. I have previously helped another user determine that their system was
of insufficient size, i.e. the water layer above and below the bilayer
was too small, and they were seeing artefacts of periodic boundaries
(the lipid headgroups were "seeing" each other and were distorting
accordingly.
Assure that your system is of adequate dimensions to eliminate
possibility #2, and otherwise just run a few ns of MD and see if the
lipids equilibrate.
-Justin
> Earlier I have run similar system with ffgmx FF with similar time 50
> ps restrain that structure pretty fine.The idea of simulating system
> with short time is if it runs fine with short time I will give long step.
>
> Toplogy file is
>
> ; Include forcefield parameters
> #include "ffoplsaa.itp"
> #include "popc.itp"
>
> [ moleculetype ]
> ; Name nrexcl
> Protein 3
>
> [ atoms ]
> ; nr type resnr residue atom cgnr charge mass typeB
> chargeB massB
> 1 opls_287 1 ALA N 1 -0.3 14.0067 ;
> qtot -0.3
> 2 opls_290 1 ALA H1 1 0.33 1.008 ;
> qtot 0.03
> 3 opls_290 1 ALA H2 1 0.33 1.008 ;
> qtot 0.36
> 4 opls_290 1 ALA H3 1 0.33 1.008 ;
> qtot 0.69
> 5 opls_293B 1 ALA CA 1 0.25 12.011 ;
> qtot 0.94
> 6 opls_140 1 ALA HA 1 0.06 1.008 ; qtot 1
> 7 opls_135 1 ALA CB 2 -0.18 12.011 ;
> qtot 0.82
> 8 opls_140 1 ALA HB1 2 0.06 1.008 ;
> qtot 0.88
> 9 opls_140 1 ALA HB2 2 0.06 1.008 ;
> qtot 0.94
> 10 opls_140 1 ALA HB3 2 0.06 1.008 ;
> qtot 1
> 11 opls_235 1 ALA C 3 0.5 12.011 ;
> qtot 1.5
> 12 opls_236 1 ALA O 3 -0.5 15.9994 ;
> qtot 1
> 13 opls_238 2 VAL N 4 -0.5 14.0067 ;
> qtot 0.5
> 14 opls_241 2 VAL H 4 0.3 1.008 ;
> qtot 0.8
> 15 opls_224B 2 VAL CA 4 0.14 12.011 ;
> qtot 0.94
> 16 opls_140 2 VAL HA 4 0.06 1.008 ; qtot 1
> .
> .
> .
> .
> .
> .
> .
> .
> .
> .
> ; Include Position restrain protein
> #ifdef POSRES_PROTEIN
> #include "posre.itp"
> #endif
>
> ;Include Position restrain lipid
> #ifdef POSRES_LIPID
> #include "lip_posre.itp"
> #endif
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; Name
> GROtesk MACabre and Sinister in water
>
> [ molecules ]
> ; Compound #mols
> Protein 1
> POPC 94
> SOL 2434
> CL- 3
>
> Any comments wiill be appreciated.
>
> Thanks in advance
>
>
>
>
>
>
> On Tue, 01 Jul 2008 Justin A.Lemkul wrote :
> >
> >
> >minnale wrote:
> >>
> >>
> >> So I dont boughter about those sentences because I confirmed in
> list archives that I can proceed further steps and moreover em.gro
> file is fine, so I went for restrain, here I am getting abnormal
> POPC structure
> >>means POPC tails are tilting, water molecules structure also disturbed.
> >>
> >>Could you please tell me where iam doing mistake?
> >>
> >
> >Not really. You haven't told us much. What parameters are you using
> (for the protein and the lipids)? How did you insert your protein?
> >
> >Also realize that 50 ps is *extremely* short in the realm of membrane
> protein MD. Even after several hundred picoseconds things may look a
> bit strange. Prevailing wisdom is that between 25-30 ns of MD are
> required for the lipids to reach equilibrium (although they should
> look reasonable after just a few ns, but parameters like area per
> headgroup may not level off for a while).
> >
> >-Justin
> >
> >>my pr.mdp filetitle = protein in popc restrained
> >>define = -DPOSRES_protein
> >>constraints = all-bonds
> >>integrator = md
> >>dt = 0.002 ; ps !
> >>nsteps = 10000 ; total 50 ps.
> >>nstcomm = 1
> >>nstxout = 50
> >>nstvout = 1000
> >>nstfout = 0
> >>nstlog = 10
> >>nstenergy = 10
> >>nstlist = 10
> >>ns_type = grid
> >>rlist = 0.9
> >>coulombtype = PME
> >>rcoulomb = 0.9
> >>rvdw = 1.4
> >>pbc = xyz
> >>; Berendsen temperature coupling is on in three groups
> >>Tcoupl = Berendsen
> >>tc-grps = POPC Protein SOL_CL-
> >>tau_t = 0.1 0.1 0.1
> >>ref_t = 310 310 310
> >>; Anisotropic pressure coupling is now on
> >>Pcoupl = berendsen
> >>pcoupltype = anisotropic
> >>tau_p = 1.0 1.0 1.0 0 0 0
> >>compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0
> >>ref_p = 1.0 1.0 1.0 0 0 0
> >>; Energy monitoring
> >>energygrps = POPC Protein SOL_CL-
> >>; Generate velocites is on at 300 K.
> >>gen_vel = yes
> >>gen_temp = 310.0
> >>gen_seed = 173529
> >>
> >>Thanks in advance.
> >>
> >>
> >>------------------------------------------------------------------------
> >>
> >>_______________________________________________
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> >
> >-- ========================================
> >
> >Justin A. Lemkul
> >Graduate Research Assistant
> >Department of Biochemistry
> >Virginia Tech
> >Blacksburg, VA
> >jalemkul[at]vt.edu | (540) 231-9080
> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> >========================================
> >
>
>
>
> ------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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